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Genet Med. 2017 May;19(5):575-582. doi: 10.1038/gim.2016.152. Epub 2016 Nov 3.

A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories.

Author information

1
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
2
Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.
3
Division of Medical Genetics, University of Washington, Seattle, Washington, USA.
4
GeneDx, Inc., Gaithersburg, Maryland, USA.
5
Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
6
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
7
Ambry Genetics, Aliso Viejo, California, USA.
8
Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, California, USA.
9
Department of Pediatrics, Columbia University, New York, New York, USA.
10
Department of Medicine, Columbia University, New York, New York, USA.
11
Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, USA.
12
Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.
13
Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA.
14
Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
15
Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA.
16
Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA.
17
Department of Internal Medicine, Center for Bioethics Social Science and Medicine, University of Michigan, Ann Arbor, Michigan, USA.
18
Illumina, Inc., San Diego, California, USA.
19
Emory Genetics Laboratory, Department of Human Genetics, Emory University, Atlanta, Georgia, USA.
20
Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, Maryland, USA.
21
Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, Massachusetts, USA.
22
Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.
23
Personalis, Inc., Menlo Park, California, USA.
24
Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.
25
Department of Molecular and Medical Genetics, Oregon Health &Science University, Portland, Oregon, USA.
26
Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
27
Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
28
Consortium on Law and Values in Health, Environment &the Life Sciences, Law School, Medical School, University of Minnesota, Minneapolis, Minnesota, USA.
29
Department of Molecular and Human Genetics, Baylor College of Medicine and Baylor Miraca Genetics Laboratories, Houston, Texas, USA.
30
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
31
Department of Pathology, Brigham &Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.

Abstract

PURPOSE:

While the diagnostic success of genomic sequencing expands, the complexity of this testing should not be overlooked. Numerous laboratory processes are required to support the identification, interpretation, and reporting of clinically significant variants. This study aimed to examine the workflow and reporting procedures among US laboratories to highlight shared practices and identify areas in need of standardization.

METHODS:

Surveys and follow-up interviews were conducted with laboratories offering exome and/or genome sequencing to support a research program or for routine clinical services. The 73-item survey elicited multiple choice and free-text responses that were later clarified with phone interviews.

RESULTS:

Twenty-one laboratories participated. Practices highly concordant across all groups included consent documentation, multiperson case review, and enabling patient opt-out of incidental or secondary findings analysis. Noted divergence included use of phenotypic data to inform case analysis and interpretation and reporting of case-specific quality metrics and methods. Few laboratory policies detailed procedures for data reanalysis, data sharing, or patient access to data.

CONCLUSION:

This study provides an overview of practices and policies of experienced exome and genome sequencing laboratories. The results enable broader consideration of which practices are becoming standard approaches, where divergence remains, and areas of development in best practice guidelines that may be helpful.Genet Med advance online publication 03 Novemeber 2016.

PMID:
27811861
PMCID:
PMC5415437
DOI:
10.1038/gim.2016.152
[Indexed for MEDLINE]
Free PMC Article

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